New: CloudBioLinux packages are now listed on biogems.info !

# biogem description by cite version released stars issues source build total 90d*) 7d   90d**)
downloads commits
bio
Bioinformatics library (...) !
BioRuby project
17 months
30
19
74690
7756
Parser of scientific names (...) !
Dmitry Mozzherin
12 weeks
16
5
39659
2635
Basic spreadsheet content extraction using apache poi (...)
Stuart Owen, Finn Bacall
7 months
5
1
33834
3307
Biogem is a software generator for Ruby in (...) !
Raoul J.P. Bonnal, Pjotr Prins
5 months
14
11
32116
1725
0
0
Binder of samtools for Ruby, on the top (...) !
Ricardo Ramirez-Gonzalez, Dan MacLean, Raoul J.P. Bonnal
2 weeks
17
5
27107
2021
0
0
Support for interacting with taverna 2 server (...) !
Robert Haines, Finn Bacall
5 weeks
2
...
23583
2975
The Ruby ucsc api: accessing the ucsc genome (...) !
Hiroyuki Mishima, Jan Aerts
7 months
13
1
20427
1306
Http requests to entrez e-utilities (...)
Jared Ning
3 years
4
...
20137
959
0
0
Gadgets for bioinformatics (...)
Shintaro Katayama
16 months
...
18678
1650
Support for interacting with taverna 2 workflows (...) !
Finn Bacall, Robert Haines, David Withers et al.
7 months
...
17692
2734
Blast search made easy! (...) !
Anurag Priyam, Ben J Woodcroft, Yannick Wurm
9 months
30
22
16860
983
0
140
Gff3 parser for big data (...) !
Pjotr Prins
2 years
6
2
16061
769
0
0
Maf parser for BioRuby (...)
Clayton Wheeler
2 years
10
30
14521
945
0
0
Interfaces with biomodel search engine (...) !
Niall Beard
2 years
...
13631
625
0
0
Create pretty svg-format images of features, gene models (...)
Dan MacLean
9 months
9
5
12835
1229
A biogem to submit jobs on a queue (...)
Francesco Strozzi
2 years
5
...
12463
902
Log4r wrapper with extra features for roles and (...) !
Pjotr Prins
2 years
4
2
12138
942
0
0
A simple obo file handler (...) !
mjy
3 years
4
...
12070
457
Very fast parallel blast xml to rdf/html/json/yaml/csv transformer (...) !
Pjotr Prins
7 weeks
11
...
10454
1346
0
57
A fast parser for fastq files (...)
Francesco Strozzi
2 years
9
...
9314
564
0
0
Support for multiple sequence alignments (msa) (...)
Pjotr Prins
5 months
6
5
9012
547
Swiss army knife of tabulated data; transforming/filtering tab/csv (...)
Pjotr Prins
5 months
7
20
8542
708
0
0
Pipeline to remove contaminations from est libraries (...)
Philipp Comans
2 years
1
1
8015
392
0
0
A tool to classify and manipulate pfemp1 dbl-alpha (...)
George Githinji
20 months
1
...
7849
469
A nexus file format (phylogenetic inference) parser in (...) !
mjy
3 years
1
...
7828
262
0
0
Low memory sequence emitters (...)
Pjotr Prins
5 months
8
1
7420
459
0
0
Build genome output files (...)
Michael Barton
14 months
3
...
7353
297
0
0
BioRuby assembly plugin (...) !
Chase Miller, Francesco Strozzi
3 years
4
...
7082
320
0
0
Simple morphbank (http://morphbank.net) services accessor (...) !
mjy
3 years
1
...
7025
270
0
0
A wrapper for the signal peptide prediction algorith (...)
Ben J Woodcroft
2 months
1
...
6839
567
Data mining algorithms for jRuby (...)
arrigonialberto86
13 months
14
3
6770
818
An open source framework for transforming heterogeneous data (...)
Joachim Baran, Kevin B. Cohen, Geraint Duck et al.
3 days
8
2
6710
680
A BioRuby plugin for interaction with the transmembrane (...)
Ben J. Woodcroft
23 months
2
...
6575
398
BioRuby plugin for reading and writing nexml (http://nexml.org) (...) !
Rutger Vos, Anurag Priyam
2 years
7
2
6564
305
0
0
Lightweight Ruby api for ncbi eutils (...)
Joon Lee, aka seouri
16 months
8
...
6512
315
This is a development release (...) !
Pjotr Prins and Trevor Wennblom
5 years
6391
204
A BioRuby plugin for calculating the isoelectric point (...)
George Githinji, Pascal Betz
2 years
3
...
6364
316
0
0
Ruby wrapper for sambamba tool (...)
Artem Tarasov
2 years
2
...
6241
387
A biogem for counting small kmers for fingerprinting (...)
Ben J Woodcroft
17 months
5
...
6098
465
0
0
Library for visualizing genomic regions (...) !
Jan Aerts
1.4
6 years
6093
241
A BioRuby plugin: handling genomic interavals and overlaps (...)
Hiroyuki Mishima
3 years
4
...
5896
274
0
0
Bio-ngs provides a framework for handling ngs data (...)
Francesco Strozzi, Raoul J.P. Bonnal
2 years
29
14
5669
274
0
0
Ruby support for the baclava file format (...) !
Robert Haines
8 months
1
...
5546
2198
Running and parsing of the protein transmembrane domain (...)
Ben J Woodcroft
3 years
1
...
5405
231
Gene ontology (go) interface for Ruby (...)
Ben J Woodcroft
3 years
9
...
4712
168
Ruby binding for bwa mapping software (...) !
Francesco Strozzi
3 years
4
...
4705
253
Reading/writing bgzf blocks (...)
Artem Tarasov, Clayton Wheeler
2 years
2
...
4696
318
0
0
A plugin that allows you to parse large (...)
robsyme
3 years
1
...
4500
238
Api to ensembl databases (...) !
Jan Aerts, Francesco Strozzi
3 years
30
5
4441
141
0
0
Iterate through a samtools pileup file (...)
Ben J. Woodcroft
23 months
2
...
4310
229
0
0
Supports linking of models within a ror application (...) !
Stuart Owen, Quyen Nguyen
2.2
7 months
...
4273
2387
0
0
Read and manipulate cd-hit clusters (...)
George Githinji
18 months
2
1
4056
304
0
0
Basespace Ruby sdk is a Ruby based software (...)
Joachim Baran, Raoul Bonnal, Eri Kibukawa et al.
14 months
11
2
3788
743
0
0
Ruby binding for samtools tabix (...)
throwern
13 months
3
...
3781
330
Geneexpression illuminahumanannotation (...)
Raoul J.P. Bonnal
3 years
1
...
3617
163
Implementation of the plasmoap algorithm (...)
Ben J Woodcroft
2 years
1
...
3584
156
Ruby wrapper for the gff3-pltools (...)
Marjan Povolni
2 years
3486
230
Chembl rest api client, parser and container (...)
Mitsuteru Nakao
2 years
1
1
3418
231
Ruby binding to the ucsc kent utilities (...)
throwern
2 years
2
...
3415
239
0
0
Next-generation mapping of mutations (...)
Dan MacLean
23 months
2
...
3406
244
Bioinformatics triple-store support (...)
Pjotr Prins
2 years
4
1
3315
177
Parse affymetrix cel/cdf files (...)
Pjotr Prins
2 years
2
1
3272
184
BioRuby core plugins, most and stable plugins. blastxmlparser, (...) !
Raoul J.P. Bonnal
3 years
1
...
3062
152
Taverna player is a rails plugin to run (...)
Robert Haines
5 weeks
4
3
2949
527
Programmatic interface to the cnls nuclear localisation signal (...)
Ben J. Woodcroft
2 years
1
...
2887
159
0
0
Enables the localisation predictor wolf psort to be (...)
Ben J Woodcroft
2 years
1
...
2832
154
Tool to work with polyploids, ngs and molecular (...)
Ricardo H.  Ramirez-Gonzalez
2 days
1
...
2644
1605
BioRuby plugin for unichem rest web service (...)
Mitsuteru Nakao
20 months
...
2637
225
Timeseries modules for statsample (...)
Ankur Goel, Claudio Bustos
13 months
...
2552
300
Reports whether a nucleotide change results in synonymous (...)
Dan MacLean
17 months
...
2516
224
Parse pfam hmm definition files (...)
Ben J. Woodcroft
2 years
1
...
2501
162
0
0
This biogem is built around krona, a flashy (...)
Ben J. Woodcroft
14 months
1
...
2491
235
A protparam compatible utility for BioRuby (...)
hryk
22 months
1
...
2444
161
Bio-gag is a biogem for detecting and correcting (...)
Ben J Woodcroft
24 months
2
...
2344
155
0
0
Parser to work with file formats used in (...)
Ben J Woodcroft
3 months
...
2050
498
Publish scientific results to the semantic web (...) !
Will Strinz
4 months
3
16
1940
221
0
5
BioRuby plugin for sun grid engine (...) !
Toshiaki Katayama
3 years
4
...
1888
89
Hello world plugin for the BioRuby (just for (...)
Toshiaki Katayama
3 years
3
...
1865
81
Digests dna based on restriction enzyme cut patterns (...) !
Trevor Wennblom
3 years
1
1862
82
Does high pairwise alignment of sequencing reads with (...)
John T. Prince
4 years
1
...
1799
69
Fast multi-threaded vcf parser (...)
Pjotr Prins
5 weeks
13
8
1750
681
3
53
Rubybhl is a simple request/response wrapper for the (...) !
Matt Yoder
8 months
6
...
1681
91
A method to get the nucleotide sequence of (...)
Ben J Woodcroft
3 years
1
...
1612
86
0
0
BioRuby core ext: plugins which require external library (...) !
Raoul J.P. Bonnal, Pjotr Prins
3 years
1
...
1606
81
0
0
Restriction enzyme dataset (...) !
Sir Richard J. Roberts, Trevor Wennblom
3 years
...
1573
85
0
0
Meta package for biolinux distribution (...) !
Raoul J.P. Bonnal
3 years
2
...
1564
90
0
0
A Ruby api to the ensembl database (...) !
Jan Aerts, Francesco Strozzi
2 years
3
...
1555
86
0
0
One-line summary of your gem (...)
Toshiaki Katayama
2 years
1
...
1536
80
Decoding the dbsnp bitfield (...)
Hiroyuki Mishima
2 years
4
...
1518
90
0
0
Phyloxml plugin for BioRuby (...)
Diana Jaunzeikare, Clayton Wheeler
2 years
3
...
1500
85
0
0
Wrapper around the exportpred algorithm for predicting p (...)
Ben J Woodcroft
2 years
1
...
1482
79
A simple biogem that allows computation of the (...)
Ben J Woodcroft
2 years
1
...
1468
84
0
0
Hydropathy scale for BioRuby (...)
Ben J Woodcroft
2 years
1
...
1456
87
A general purpose framework for scripted handling of (...) development/stable
mjy
19 months
1
...
1410
84
Ruby solution for ucsc liftover tool- (ucsc http://genome.ucsc.edu/cgi-bin/hgliftover) (...)
Andrei Rozanski
7 months
1
...
1406
321
Gggenome Ruby client (...)
Mitsuteru Nakao
14 months
1
...
1369
156
0
0
Enables parsing of hmmer version 3 reports (...)
Christian Zmasek, Ben J Woodcroft
2 years
1
1
1348
89
0
0
Biological extensions for the intermine webservice client library (...) !
Alex Kalderimis
3 years
...
1293
54
0
0
Ruby ensembl rest api (...)
Alberto Donizetti
13 months
3
1
1283
158
0
0
Build graph with jRuby (...)
Matteo Picciolini
2 years
...
1259
88
A programmatic interface to the ipcress in-silico pcr (...)
Ben J Woodcroft
2 years
1
...
1255
87
Generalized linear models for statsample (...)
Ankur Goel
13 months
...
1233
155
Server for polymarker. to be used with cron (...)
Ricardo H.  Ramirez-Gonzalez
2 weeks
...
1102
787
Reads metadata from integrated microbial genomes (img) metadata (...)
Ben J. Woodcroft
21 months
...
1004
83
Biostars data-mining and statistical analysis (...)
Joachim Baran
6 months
...
997
253
0
0
Dead simple method of running shell commands from (...)
Ben J. Woodcroft
9 months
...
971
173
0
0
Interface for express beta diversity (...)
Ben J. Woodcroft
9 months
...
942
172
0
0
Bio-repeatmasker (...)
Andrei Rozanski
9 months
933
167
Parse stockholm sequence alignment format (...)
Ben J. Woodcroft
16 months
2
...
792
85
0
0
A parser for cigar format alignments (...)
Ben J Woodcroft
8 months
4
...
781
167
0
0
Ruby wrapper to run standard-raxml for maximum likelihood (...)
Fernando Izquierdo
15 months
...
728
90
0
0
Bindings to some internals of the velvet assembler (...)
Ben Woodcroft
5 months
1
690
166
Client for xoopit's cloudquery api (...)
Cameron Walters, nb.io
5 years
4
...
660
660
0
0
Web server for bio-samtools (...)
homonecloco
5 months
...
636
174
0
0
Fast storage and comparison of chr+pos(+alt) locations (...)
Pjotr Prins
2 weeks
...
406
205
Mine publications for gene names (...)
Pjotr Prins
8 months
...
392
86
Pass a full citation, get the bibtex back, (...) !
Matt Yoder
4 weeks
...
374
374
0
6
(...) pre
pre
366
15
Csshttprequest is cross-domain ajax using css as a (...)
Cameron Walters, Randy Reddig
5 years
30
1
330
330
A restful service for sharing genomic data (...) !
Joachim Baran, Robert Buels, Michel Dumontier
7 months
2
...
316
63
Ruby inferface for kseq.h by heng li for (...)
Fedor Gusev
3 months
...
230
109
Csshttprequest is cross-domain ajax using css (...)
Cameron Walters, Randy Reddig
0.1
5 years
172
172
A Ruby wrapper on the open tree api (...) beta
Matt Yoder
5 weeks
...
145
80
0
22
!
Tools to manipulate blat files from the command (...) new
homonecloco
3 weeks
...
136
136
0
6
!
Tools to work with fasta files, indexed with (...) new
homonecloco
3 weeks
...
130
130
(...) pre
pre
99
19
*) gem downloads (total & last 90 days) from rubygems.org as of 2014-10-30
**) number of commits on GitHub (last 7 days & last 90 days)